My first ever repository, some notebooks useful, others sucks. Topics include file format conversion with obabel, docking with Auto Dock, MD with Charmm GUI and QSAR etc, never expect the format is perfect.
☆26Oct 22, 2025Updated 9 months ago
Alternatives and similar repositories for notebook
Users that are interested in notebook are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- To run metadynamics simulations using openMM (based on Peter Eastman's script)☆13Mar 18, 2019Updated 7 years ago
- Workshops on Computational Biology organized by our lab☆10Mar 25, 2024Updated 2 years ago
- Accelerating Metadynamics-Based Free-Energy Calculations with Adaptive Machine Learning Potentials☆18Jun 9, 2021Updated 5 years ago
- Enhanced protein mutational sampling using time-lagged variational autoencoders☆30Sep 17, 2018Updated 7 years ago
- Codes to use funnel-metadynamics and funnel metadynamics automated protocol☆31Dec 19, 2021Updated 4 years ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Python code that takes a SDF file as input to calculate the central nervous system multiparameter optimization (CNS MPO) score☆11Oct 23, 2018Updated 7 years ago
- Generate Ramachandran plots for single PDB structure and as heatmap for MD trajectory☆11Apr 6, 2022Updated 4 years ago
- Materials from the Intro to the RDKit tutorial at AIDD 2021☆20Oct 19, 2021Updated 4 years ago
- GitHub for AI4PD 2023 Workshop in Chile☆12Oct 12, 2023Updated 2 years ago
- Quickstart Python tutorials helping molecular dynamics practitioners get up to speed with OpenMM☆52Aug 26, 2017Updated 8 years ago
- notebook repository☆13Jan 17, 2022Updated 4 years ago
- Rethinking Metadynamics: From Bias Potentials to Probability Distributions☆15Sep 18, 2023Updated 2 years ago
- ChEMBL Database used to create Lipinski Descriptors (ADME Pharmokinetic Profile) to use in a Random Forest Regression Model☆15Nov 8, 2020Updated 5 years ago
- A Motif-Based PPI Searching Pipeline for PPI Mining and Protein Design☆21Feb 11, 2025Updated last year
- End-to-end encrypted cloud storage - Proton Drive • AdSpecial offer: 40% Off Yearly / 80% Off First Month. Protect your most important files, photos, and documents from prying eyes.
- Probabilistic Multi-Parameter Optimization (pMPO)☆17Apr 7, 2017Updated 9 years ago
- Useful Collective Variables for OpenMM☆18May 9, 2024Updated 2 years ago
- Input files and binding free energy values from our benchmark with QuantumBind-RBFE☆16Apr 16, 2025Updated last year
- The Biochemical Library (BCL) integrates traditional small molecule cheminformatics tools with machine learning-based quantitative struct…☆37Feb 14, 2024Updated 2 years ago
- ☆15Jun 21, 2022Updated 4 years ago
- Open Source, Automated free binding free energy calculation between protein and small molecule. An all-in-one workflow, free energy pertu…☆59Apr 21, 2025Updated last year
- Using neural networks for enhanced sampling in computational biophysics☆16Aug 17, 2017Updated 8 years ago
- EViS: an Enhanced Virtual Screening Approach based on Pocket Ligand Similarity☆14Dec 7, 2021Updated 4 years ago
- ☆22Dec 15, 2024Updated last year
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- ☆14Mar 7, 2024Updated 2 years ago
- Statistical Analysis of Docking Results and Scoring functions☆21May 14, 2026Updated 2 months ago
- Tutorials on doing AMBER based Metadynamics and Gaussian Accelerated MD (GaMD)☆13Dec 1, 2025Updated 8 months ago
- Perform probe-guided blind docking with FTMap and DOCK6☆10Apr 25, 2023Updated 3 years ago
- Streamlined version of VirtualFlow combining both VFVS and VFLP☆22Jul 6, 2026Updated last month
- Tutorial on the setup and simulation of a membrane protein with AMBER Lipid21 and PACKMOL-Memgen☆77Aug 11, 2023Updated 3 years ago
- Building more accurate protein structures from backbone torsion angles☆16Mar 21, 2025Updated last year
- This is the public repository for the RING PyMOL plugin developed by the BioComputing UP laboratory at the University of Padua☆31Sep 17, 2025Updated 10 months ago
- Example files for Colvars module: https://github.com/Colvars/colvars☆14Dec 7, 2021Updated 4 years ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- Material to run the HADDOCK antibody-antigen modelling protocol☆23Apr 13, 2026Updated 3 months ago
- ☆32Apr 18, 2025Updated last year
- An open tool implementing some recommended practices for analyzing alchemical free energy calculations☆140May 24, 2024Updated 2 years ago
- Cryptic pocket prediction using AlphaFold 2☆25Nov 27, 2022Updated 3 years ago
- SIEVE-Score: interaction energy-based virtual screening method based on random forest.☆14Sep 15, 2023Updated 2 years ago
- ☆13Jul 11, 2023Updated 3 years ago
- binding free energy estimator 2☆146Jul 29, 2026Updated 2 weeks ago